1. We have carried out an equilibrium ultracentrifugation study of five DNA dodecamers four of which contain purine-purine mispairs. At temperatures below the main order-disorder transition, solutions of these DNA molecules are equilibrium mixtures of organized monomeric hairpin and double helical molecules. The finding of hairpin molecules has: a) led to the inference based upon optical melting data that two base pair loops are possible in DNA b) led to a satisfactory and self-consistent thermodynamic analysis of the melting transition which by inclusion of the helix-hairpin equilibrium results in reasonable values of the associated thermodynamic parameters as opposed to unreasonable values obtained by assuming an oversimplified two-state model for the transition. 2. We have completed to thermodynamically rigorous computation that elucidates the underlying causes of complex bimodal and polymodal excess heat capacity vs. temperature profiles for the thermal denaturation of macromolecule that may bind and arbitrary number of ligand molecules to either and/or both the native and denatured states between which there may also be a finite difference in heat capacity. These calculations account essentially completely for experimental data we have obtained and demonstrate that complex thermograms can arise from the melting of structural domains with in the macromolecule. 3. We have measured the heat of reaction between the repressor protein cro and six different 21 bp DNA oligonucleotides between 5 degrees and 37 degrees. The DNA sequences include two specific operator sequences OR1 and OR3, two completely "non-specific" sequences and two sequences of intermediate affinity. The enthalpy changes are proportional to the affinity for DNA and are endothermic at low temperature becoming exothermic above 25 degrees. The magnitudes of the enthalpy changes are surprisingly small considering the wide area of contact between protein and DNA.